Median Tectonic Line (MTL) and Fossa Magna (Itoigawa-Shizuoka Tectonic Line) had long been considered to be the most critical fault boundaries controlling development of the Japanese Islands since Naumann (1885) and Kobayashi (1941). After the appearance of plate tectonics, several new interpretations emerged, <i>e.g.</i>, sub-surface Benioff plane for the MTL. In this paper, we propose that those tectonic lines, major faults, and Tanakura Tectonic Line (TTL) were formed through a process at micro-plate boundaries during the opening of the Japan Sea in the Miocene.<br> MTL could have been formed along the consuming boundary between the PHS plate and Japan Sea microplate, which has shifted southward to the Nankai trough, accompanying large-scale tectonic erosion. Fossa Magna was formed as a gigantic transform fault with a transtension component in the Medial-Japan Sea when opening was initiated. The eastern and western boundaries of the Japan Sea must be a strike-slip fault, corresponding to TTL to the east, and a newly proposed strike-slip fault called the West Kyushu Tectonic Line, respectively. Fossa Magna, a medial region defined by two NS-trending Miocene parallel faults in central Honshu, defined by Nauman (1885) could be interpreted to be the largest transform fault in the Medial-Japan Sea to offset the spreading axis when the Japan Sea opened.<br> It should be emphasized that large-scale tectonic erosion occurred in front of consuming plate boundaries facing the PHS and PAC plates oceanward during the opening of the Japan Sea. The volume of tectonic erosion is calculated to be 17,581,500 km<sup>3</sup>, which is equivalent to 2/3 of the present-day Japan arc crust, which is sufficient to reach the depth of the megalith between the upper and lower mantle boundary, even with 10 km thickness of materials eroded and transported along the Benioff zone.<br> Although MTL, Fossa Magna, and TTL are remarkable in the geology of Japan, these young faults never affected the orogeneses of Japan back to 520 Ma, which grew the continental crust of Japan. We propose that microplate boundary processes decreased the volume of the Japan crust.